Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 100 of 438
Found at i:28276326 original size:16 final size:16
Alignment explanation
Indices: 28276305--28276346 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
28276295 TGAATCCTTA
28276305 AAATCTTAAAATCCCT
1 AAATCTTAAAATCCCT
* *
28276321 AAATCTTGAAATCCTT
1 AAATCTTAAAATCCCT
28276337 AAATCATTAA
1 AAATC-TTAA
28276347 CATTCCGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATCTTAAAATCCCT
Found at i:28276804 original size:116 final size:116
Alignment explanation
Indices: 28276530--28276853 Score: 470
Period size: 116 Copynumber: 2.8 Consensus size: 116
28276520 GTTTTGTTGA
*
28276530 TTATTTTTGATTTATTATTGCAATTTTAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGTGAT
1 TTATTTGTGATTTATTATTGCAATTTTAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGTGAT
* *
28276595 GCAACAGTGGTCTCGATGTTGTTGATAAAATTATTGCTAAAATTGTAGATAG
66 GCGACAGTGGTC-CAATGTTGTTGATAAAATTATTGCTAAAATTGTAGATAG
*
28276647 TTATTTGTGATTTATTATTGCAATTTTAGTGCCACAATGTAGGGTTTGTTTTGTCAATTTGTGAT
1 TTATTTGTGATTTATTATTGCAATTTTAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGTGAT
* * * * * *
28276712 ACGACAATGGTCCAATGTTATTGAT-AAATCTGTTGTTAAAATTGTAGATGG
66 GCGACAGTGGTCCAATGTTGTTGATAAAAT-TATTGCTAAAATTGTAGATAG
* * * * * *
28276763 TTATTTGTGATTTATTTTTACAATTTCAATGCCACAATGTAGGGTTTATTTTTTCGATTTGTGAT
1 TTATTTGTGATTTATTATTGCAATTTTAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGTGAT
28276828 GCGACAGTGGTCCCAATGTTGTTGAT
66 GCGACAGTGGT-CCAATGTTGTTGAT
28276854 TTCTGTTACC
Statistics
Matches: 185, Mismatches: 20, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
115 4 0.02
116 96 0.52
117 85 0.46
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.45
Consensus pattern (116 bp):
TTATTTGTGATTTATTATTGCAATTTTAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGTGAT
GCGACAGTGGTCCAATGTTGTTGATAAAATTATTGCTAAAATTGTAGATAG
Found at i:28277391 original size:33 final size:33
Alignment explanation
Indices: 28277354--28277422 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
28277344 TGTTGACTAC
* *
28277354 TGGGGAGGGTGATGTTGATGGGGTAGAAGT-TGA
1 TGGGGAGGGTGATGATGAAGGGGTAGAA-TCTGA
28277387 TGGGGAGGGTGATGATGAAGGGGTAGAATCTGA
1 TGGGGAGGGTGATGATGAAGGGGTAGAATCTGA
28277420 TGG
1 TGG
28277423 TGAAAGTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.23, C:0.01, G:0.51, T:0.25
Consensus pattern (33 bp):
TGGGGAGGGTGATGATGAAGGGGTAGAATCTGA
Found at i:28277432 original size:33 final size:33
Alignment explanation
Indices: 28277362--28277450 Score: 83
Period size: 33 Copynumber: 2.7 Consensus size: 33
28277352 ACTGGGGAGG
* * **
28277362 GTGATGTTGATGGGGTAGAAGT-TGATGGGGAGG
1 GTGATGATGAAGGGGTAGAA-TCTGATGGGGAAA
*
28277395 GTGATGATGAAGGGGTAGAATCTGATGGTGAAA
1 GTGATGATGAAGGGGTAGAATCTGATGGGGAAA
* *
28277428 GTGAT-CTAGAAAGGGTAGAATCT
1 GTGATGAT-GAAGGGGTAGAATCT
28277451 ATTGAAGAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 2 0.04
33 45 0.96
ACGTcount: A:0.29, C:0.03, G:0.42, T:0.26
Consensus pattern (33 bp):
GTGATGATGAAGGGGTAGAATCTGATGGGGAAA
Found at i:28277477 original size:33 final size:35
Alignment explanation
Indices: 28277391--28277486 Score: 80
Period size: 33 Copynumber: 2.9 Consensus size: 35
28277381 AGTTGATGGG
*
28277391 GAGGGTGATGAT-GAAGGGGTAGAATCTGATGGTGAA
1 GAGGGTGAT-ATAAAAGGGGTAGAATCTGAT-GTGAA
*
28277427 -A--GTGATCTAGAAA-GGGTAGAATCT-AT-TGAA
1 GAGGGTGATATA-AAAGGGGTAGAATCTGATGTGAA
* *
28277457 GAGGGTGATATAAAAGGGGTACAAGCTGAT
1 GAGGGTGATATAAAAGGGGTAGAATCTGAT
28277487 AGAGAGGGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
30 4 0.08
31 1 0.02
32 6 0.12
33 32 0.67
34 4 0.08
35 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.36, T:0.23
Consensus pattern (35 bp):
GAGGGTGATATAAAAGGGGTAGAATCTGATGTGAA
Found at i:28281639 original size:40 final size:40
Alignment explanation
Indices: 28281501--28281641 Score: 187
Period size: 40 Copynumber: 3.5 Consensus size: 40
28281491 ACCCAAGTTT
* * * *
28281501 CTTCGGGAT-TTAG-CCGGATATAACCACACGCCCAATTGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAATGC
* * *
28281540 CTTCGGGTCTTAACCCGGACATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
28281580 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
*
28281620 CTTCGGGGCTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
28281642 CATTCAAATG
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
38 1 0.01
39 10 0.11
40 78 0.88
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
Found at i:28289569 original size:40 final size:40
Alignment explanation
Indices: 28289489--28289709 Score: 347
Period size: 40 Copynumber: 5.5 Consensus size: 40
28289479 ACCCAAGTTT
* * * *
28289489 CTTCGGGAT-TTAG-CCGGATATAACCACACGCCCAATTGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAATGC
* * *
28289528 CTTCGGGTCTTAACCCGGACATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
28289568 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
28289608 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
28289648 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
*
28289688 CTTCGGGGCTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
28289710 CATTCAAATG
Statistics
Matches: 169, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
38 1 0.01
39 10 0.06
40 158 0.93
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
Found at i:28291029 original size:29 final size:29
Alignment explanation
Indices: 28290987--28291044 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28290977 AACATGAGAA
28290987 AGACTCCTTTGTTTCTTTTCTCTTTTCCT
1 AGACTCCTTTGTTTCTTTTCTCTTTTCCT
28291016 AGACTCCTTTGTTTCTTTTCTCTTTTCCT
1 AGACTCCTTTGTTTCTTTTCTCTTTTCCT
28291045 TATTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.07, C:0.28, G:0.07, T:0.59
Consensus pattern (29 bp):
AGACTCCTTTGTTTCTTTTCTCTTTTCCT
Found at i:28310892 original size:51 final size:51
Alignment explanation
Indices: 28310815--28310954 Score: 151
Period size: 51 Copynumber: 2.7 Consensus size: 51
28310805 TGGATGCCCG
* * * *
28310815 GTGGCCTGCACATAATACCACCCTTGTAGTC-AAAGCTACCTTCTT-CACAAA
1 GTGGCCTACACATAGTACCACACTTGT-GACGAAAGCTACCTT-TTACACAAA
* * *
28310866 GTGGCCTTCACATAGTACCACACTTGTGACGAAAGCTATCTTTTACACATA
1 GTGGCCTACACATAGTACCACACTTGTGACGAAAGCTACCTTTTACACAAA
* *
28310917 GTGGCCTACACTTAGTACCACACATGTGATCG-AAGCTA
1 GTGGCCTACACATAGTACCACACTTGTGA-CGAAAGCTA
28310955 TCTGTAACAA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
50 4 0.05
51 71 0.92
52 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (51 bp):
GTGGCCTACACATAGTACCACACTTGTGACGAAAGCTACCTTTTACACAAA
Found at i:28317783 original size:48 final size:48
Alignment explanation
Indices: 28317713--28317926 Score: 216
Period size: 48 Copynumber: 4.5 Consensus size: 48
28317703 ACAGCCCAAC
* * * * *
28317713 TATGGTCTTACAC-GAAGTCTCATAACGGTGCCGATGTCATGTCCCAGA
1 TATGGTCTTATACGGGA-TCTCATAACGATGCCGATGCCATATCCCAGA
* * * * *
28317761 CATGGTCTTATACGGGACCTCATATCGATGCCAATGCCATATCCCATA
1 TATGGTCTTATACGGGATCTCATAACGATGCCGATGCCATATCCCAGA
* * *
28317809 AATGGTCTTACATGGGATCTCAT-ACTGATGCCGATGCCATATCCCAGA
1 TATGGTCTTATACGGGATCTCATAAC-GATGCCGATGCCATATCCCAGA
* * *** * *
28317857 TATGGGCTTATACGAGATCTCATTTTGATGCCGATGTCATATCCTAGA
1 TATGGTCTTATACGGGATCTCATAACGATGCCGATGCCATATCCCAGA
28317905 TATGGTCTTATACGGGATCTCA
1 TATGGTCTTATACGGGATCTCA
28317927 ATACTCACAT
Statistics
Matches: 135, Mismatches: 28, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
47 1 0.01
48 132 0.98
49 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (48 bp):
TATGGTCTTATACGGGATCTCATAACGATGCCGATGCCATATCCCAGA
Found at i:28317844 original size:96 final size:97
Alignment explanation
Indices: 28317741--28317931 Score: 240
Period size: 96 Copynumber: 2.0 Consensus size: 97
28317731 CTCATAACGG
* * * *
28317741 TGCCGATGTCATGTCCCAGACATGGTCTTATACGGGACCTCATATCGATGCCAATGCCATATCCC
1 TGCCGATGCCATATCCCAGACATGGGCTTATACGAGACCTCATATCGATGCCAATGCCATATCCC
* *
28317806 ATAAATGGTCTTACATGGGATCTC-ATACTGA
66 AGAAATGGTCTTACACGGGATCTCAATACTGA
* * * * * * *
28317837 TGCCGATGCCATATCCCAGATATGGGCTTATACGAGATCTCATTTTGATGCCGATGTCATATCCT
1 TGCCGATGCCATATCCCAGACATGGGCTTATACGAGACCTCATATCGATGCCAATGCCATATCCC
* *
28317902 AGATATGGTCTTATACGGGATCTCAATACT
66 AGAAATGGTCTTACACGGGATCTCAATACT
28317932 CACATGTTGT
Statistics
Matches: 79, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
96 74 0.94
97 5 0.06
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (97 bp):
TGCCGATGCCATATCCCAGACATGGGCTTATACGAGACCTCATATCGATGCCAATGCCATATCCC
AGAAATGGTCTTACACGGGATCTCAATACTGA
Found at i:28318057 original size:6 final size:6
Alignment explanation
Indices: 28318046--28318093 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
28318036 ATAAAGACAA
28318046 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
28318094 TTCATGCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:28318862 original size:50 final size:50
Alignment explanation
Indices: 28318787--28318895 Score: 209
Period size: 50 Copynumber: 2.2 Consensus size: 50
28318777 CTTGAATATG
28318787 GACAAAAATTGGCTTTTAATTTTGTTTTTAATTCATTTTAATTACTAAAT
1 GACAAAAATTGGCTTTTAATTTTGTTTTTAATTCATTTTAATTACTAAAT
28318837 GACAAAAATTGGCTTTTAATTTTGTTTTTAATTCATTTTAATTACTAAAT
1 GACAAAAATTGGCTTTTAATTTTGTTTTTAATTCATTTTAATTACTAAAT
*
28318887 GACCAAAAT
1 GACAAAAAT
28318896 GCCCCTAACT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (50 bp):
GACAAAAATTGGCTTTTAATTTTGTTTTTAATTCATTTTAATTACTAAAT
Found at i:28319108 original size:13 final size:13
Alignment explanation
Indices: 28319090--28319115 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28319080 GCCCAAACGT
28319090 CAAAATTTTCAAA
1 CAAAATTTTCAAA
28319103 CAAAATTTTCAAA
1 CAAAATTTTCAAA
28319116 AAATCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
CAAAATTTTCAAA
Found at i:28326715 original size:40 final size:40
Alignment explanation
Indices: 28326652--28326755 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
28326642 ATTATACCTG
* * ** *
28326652 AATTACACATACGTGCCCTTGTTTGTACTTTGGTACCCCT
1 AATTGCACATACGTGCCCCTGTTTGTACTCCGATACCCCT
28326692 AATTGCACATACGCT-CCCCTGTTTGTACTCCGATACCCCT
1 AATTGCACATACG-TGCCCCTGTTTGTACTCCGATACCCCT
* *
28326732 GATTGCACATACATGCCCCTGTTT
1 AATTGCACATACGTGCCCCTGTTT
28326756 ACACTTCAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.02
40 53 0.96
41 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.34
Consensus pattern (40 bp):
AATTGCACATACGTGCCCCTGTTTGTACTCCGATACCCCT
Found at i:28330025 original size:38 final size:38
Alignment explanation
Indices: 28329928--28330030 Score: 143
Period size: 38 Copynumber: 2.7 Consensus size: 38
28329918 GGCTTAAAGA
** * *
28329928 CCCGCAGGCTTCGTGCTGGTAAAATATCCGAGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCAGAGATAAAT
*
28329966 CCCGCAGGCTTCGTGCTGGTATTATATCAGGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCAGAGATAAAT
* *
28330004 CCCGCAGGCCTAGTGCTGGTATTATAT
1 CCCGCAGGCTTCGTGCTGGTATTATAT
28330031 TCGGGCCTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.28
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTATTATATCAGAGATAAAT
Found at i:28330076 original size:43 final size:43
Alignment explanation
Indices: 28330028--28330451 Score: 336
Period size: 43 Copynumber: 9.6 Consensus size: 43
28330018 GCTGGTATTA
* *
28330028 TATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
28330071 TATTCGGGCCTTCGTACCTAGAAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
28330114 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
28330157 TATTCGGGCCTTCGTGCCGGTGATGTATATTCAGGCCTTCGTGCC--TAGCAGGCT-
1 TATTCGGGCCTTCGTGCC--T-A-G------CAGG-CTTCGTGCCGGT-G-ATG-TG
* * *
28330211 TCATGTCGGTG--AT-GTG--TATTCGGGCCTTCGTGCC--TAGCA-G-G
1 T-AT-TCGG-GCCTTCGTGCCTA-GCAGG-CTTCGTGCCGGT-G-ATGTG
* * * ** * * *
28330252 -CTTCGTGCCGGT-GATGTGTATTCGGGCCTTCGTGCCGGTGATGTA
1 TATTCGGGCC-TTCG-TGCCTA-GCAGG-CTTCGTGCCGGTGATGTG
* * **
28330297 TATTCAGGCCTTCGTGCCTAGCAGGCTTCATATCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
28330340 TATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
28330383 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
28330426 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
28330452 GTAATGCCAG
Statistics
Matches: 319, Mismatches: 32, Indels: 60
0.78 0.08 0.15
Matches are distributed among these distances:
37 1 0.00
38 3 0.01
39 1 0.00
40 2 0.01
41 2 0.01
42 1 0.00
43 255 0.80
44 5 0.02
45 7 0.02
46 8 0.03
47 1 0.00
49 2 0.01
50 1 0.00
52 1 0.00
53 5 0.02
54 15 0.05
55 4 0.01
56 4 0.01
57 1 0.00
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:28330177 original size:27 final size:27
Alignment explanation
Indices: 28330135--28330201 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
28330125 TCGTGCCTAG
*
28330135 CAGG-CTTCGTGCCGGTGATGTGTATT
1 CAGGCCTTCGTGCCGGTGATGTATATT
*
28330161 CGGGCCTTCGTGCCGGTGATGTATATT
1 CAGGCCTTCGTGCCGGTGATGTATATT
28330188 CAGGCCTTCGTGCC
1 CAGGCCTTCGTGCC
28330202 TAGCAGGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 3 0.08
27 34 0.92
ACGTcount: A:0.10, C:0.25, G:0.33, T:0.31
Consensus pattern (27 bp):
CAGGCCTTCGTGCCGGTGATGTATATT
Found at i:28330188 original size:70 final size:70
Alignment explanation
Indices: 28330096--28330244 Score: 262
Period size: 70 Copynumber: 2.1 Consensus size: 70
28330086 ACCTAGAAGG
* * *
28330096 CTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATT
1 CTTCGTGCCGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGATGTGTATT
28330161 CGGGC
66 CGGGC
*
28330166 CTTCGTGCCGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATGTCGGTGATGTGTATT
1 CTTCGTGCCGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGATGTGTATT
28330231 CGGGC
66 CGGGC
28330236 CTTCGTGCC
1 CTTCGTGCC
28330245 TAGCAGGCTT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.10, C:0.25, G:0.33, T:0.32
Consensus pattern (70 bp):
CTTCGTGCCGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGATGTGTATT
CGGGC
Found at i:28330223 original size:156 final size:153
Alignment explanation
Indices: 28330026--28330451 Score: 579
Period size: 156 Copynumber: 2.7 Consensus size: 153
28330016 GTGCTGGTAT
* *
28330026 TATATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCAGTGATGTGTATTCGGGCCTTCGTACCTA
1 TATATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
28330091 GAAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTC-GTGCCGGT-GAT
66 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCAG-GCC-GTCG-T
** * * * *
28330154 GTGTATTCGGGCCTTCGTGCCGGTGATG
128 GCCTA-GCAGG-CTTCATACCGGTGATG
* ** *
28330182 TATATTCAGGCCTTCGTGCCTAGCAGGCTTCATGTCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 TATATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* ** *
28330247 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCGGTGATGTA-TATTCAGGCCTTCG
66 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCC--T-A-GCAGGCTTCAGGCCGTCG
*
28330311 TGCCTAGCAGGCTTCATATCGGTGATG
127 TGCCTAGCAGGCTTCATACCGGTGATG
*
28330338 TGTATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 TATATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
28330403 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
66 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
28330452 GTAATGCCAG
Statistics
Matches: 237, Mismatches: 26, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
152 2 0.01
153 1 0.00
154 1 0.00
156 213 0.90
157 3 0.01
158 6 0.03
159 8 0.03
160 3 0.01
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.31
Consensus pattern (153 bp):
TATATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCAGGCCGTCGTGCC
TAGCAGGCTTCATACCGGTGATG
Found at i:28330255 original size:113 final size:113
Alignment explanation
Indices: 28330057--28330400 Score: 607
Period size: 113 Copynumber: 3.0 Consensus size: 113
28330047 AGCAGGCTTT
* * * * * * *
28330057 GTGCCAGTGATGTGTATTCGGGCCTTCGTACCTAGAAGGCTTCGTGCCGGTGATGTGTATTCGGG
1 GTGCCGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATGTCGGTGATGTGTATTCGGG
28330122 CCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTC
66 CCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTC
28330170 GTGCCGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATGTCGGTGATGTGTATTCGGG
1 GTGCCGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATGTCGGTGATGTGTATTCGGG
28330235 CCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTC
66 CCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTC
*
28330283 GTGCCGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATATCGGTGATGTGTATTCGGG
1 GTGCCGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATGTCGGTGATGTGTATTCGGG
*
28330348 CCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTC
66 CCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTC
28330396 GTGCC
1 GTGCC
28330401 TAGCAGGCTT
Statistics
Matches: 222, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 222 1.00
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.32
Consensus pattern (113 bp):
GTGCCGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATGTCGGTGATGTGTATTCGGG
CCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTC
Found at i:28330290 original size:27 final size:27
Alignment explanation
Indices: 28330248--28330314 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
28330238 TCGTGCCTAG
*
28330248 CAGG-CTTCGTGCCGGTGATGTGTATT
1 CAGGCCTTCGTGCCGGTGATGTATATT
*
28330274 CGGGCCTTCGTGCCGGTGATGTATATT
1 CAGGCCTTCGTGCCGGTGATGTATATT
28330301 CAGGCCTTCGTGCC
1 CAGGCCTTCGTGCC
28330315 TAGCAGGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 3 0.08
27 34 0.92
ACGTcount: A:0.10, C:0.25, G:0.33, T:0.31
Consensus pattern (27 bp):
CAGGCCTTCGTGCCGGTGATGTATATT
Found at i:28330291 original size:70 final size:70
Alignment explanation
Indices: 28330217--28330357 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 70
28330207 GGCTTCATGT
* * * *
28330217 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTT
1 CGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATACCGGTGATGTGTATTCGGGCCTT
28330282 CGTGC
66 CGTGC
*
28330287 CGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATATCGGTGATGTGTATTCGGGCCTT
1 CGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATACCGGTGATGTGTATTCGGGCCTT
28330352 CGTGC
66 CGTGC
28330357 C
1 C
28330358 TAGCAGGCTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.11, C:0.24, G:0.33, T:0.32
Consensus pattern (70 bp):
CGGTGATGTATATTCAGGCCTTCGTGCCTAGCAGGCTTCATACCGGTGATGTGTATTCGGGCCTT
CGTGC
Found at i:28334775 original size:31 final size:31
Alignment explanation
Indices: 28334737--28334805 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
28334727 TGTATTTAGA
28334737 TAGATTTGTTTTGGTATTCTTTGATGATATT
1 TAGATTTGTTTTGGTATTCTTTGATGATATT
28334768 TAGATTTGTTTTGGTATTCTTTGATGATATT
1 TAGATTTGTTTTGGTATTCTTTGATGATATT
*
28334799 TTGATTT
1 TAGATTT
28334806 ATTCACGGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.19, C:0.03, G:0.19, T:0.59
Consensus pattern (31 bp):
TAGATTTGTTTTGGTATTCTTTGATGATATT
Found at i:28338444 original size:120 final size:120
Alignment explanation
Indices: 28338228--28338450 Score: 286
Period size: 120 Copynumber: 1.9 Consensus size: 120
28338218 TTATACCGGA
* * *
28338228 ATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCTTGATTGAACATACGTGTCCCTTTTTGT
1 ATTGCACATACGTGACCCTATTTGTACTTCGGTACCCTTGATTGAACATACGTGCCCCTGTTTGT
* * * * * * *
28338293 ACTTCGATACCCTTGATTGCATATACGTGCCCTTGTTTGTACTTTAGTACCCCTG
66 ACATCGATACCCCTAATGGCACATACATGCCCCTGTTTGTACTTTAGTACCCCTG
* * * * *
28338348 ATTGCACATATGTGACCTTTTTTGTACTTTGGTACCCTTGATTGCACATACG-GACCCCTGTTTG
1 ATTGCACATACGTGACCCTATTTGTACTTCGGTACCCTTGATTGAACATACGTG-CCCCTGTTTG
*
28338412 TACATCGGTACCCCTAATGGCACATACATGCCCCTGTTT
65 TACATCGATACCCCTAATGGCACATACATGCCCCTGTTT
28338451 ACACTTTGGA
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
119 1 0.01
120 85 0.99
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (120 bp):
ATTGCACATACGTGACCCTATTTGTACTTCGGTACCCTTGATTGAACATACGTGCCCCTGTTTGT
ACATCGATACCCCTAATGGCACATACATGCCCCTGTTTGTACTTTAGTACCCCTG
Found at i:28338447 original size:40 final size:40
Alignment explanation
Indices: 28338228--28338450 Score: 250
Period size: 40 Copynumber: 5.6 Consensus size: 40
28338218 TTATACCGGA
*
28338228 ATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCTTG
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTTG
* * * *
28338268 ATTGAACATACGTGTCCCTTTTTGTACTTCGATACCCTTG
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTTG
* * ** *
28338308 ATTGCATATACGTGCCCTTGTTTGTACTTTAGTACCCCTG
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTTG
* * * * *
28338348 ATTGCACATATGTGACCTTTTTTGTACTTTGGTACCCTTG
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTTG
* * *
28338388 ATTGCACATACG-GACCCCTGTTTGTACATCGGTACCCCTA
1 ATTGCACATACGTG-CCCCTGTTTGTACTTCGGTACCCTTG
* *
28338428 ATGGCACATACATGCCCCTGTTT
1 ATTGCACATACGTGCCCCTGTTT
28338451 ACACTTTGGA
Statistics
Matches: 152, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 150 0.99
41 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (40 bp):
ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTTG
Found at i:28349561 original size:12 final size:12
Alignment explanation
Indices: 28349546--28349575 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28349536 ATTGGTTGTT
28349546 ACACGGCCTAAC
1 ACACGGCCTAAC
*
28349558 ACACGGCCTGAC
1 ACACGGCCTAAC
28349570 ACACGG
1 ACACGG
28349576 GCGTTTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.40, G:0.23, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAAC
Found at i:28352148 original size:20 final size:22
Alignment explanation
Indices: 28352123--28352169 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
28352113 CTTATGCTTC
*
28352123 ATTAAATACTTAATTA-TCT-A
1 ATTAAATAATTAATTACTCTCA
28352143 ATTAAATAATTAATTACTCTCA
1 ATTAAATAATTAATTACTCTCA
28352165 ATTAA
1 ATTAA
28352170 GTTATTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 15 0.62
21 3 0.12
22 6 0.25
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAAATAATTAATTACTCTCA
Found at i:28357963 original size:29 final size:29
Alignment explanation
Indices: 28357882--28357964 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 29
28357872 GTGAATGAAA
28357882 TTGGGCCTAATGGGCCATATGAATGTGAT
1 TTGGGCCTAATGGGCCATATGAATGTGAT
* *** ** *
28357911 TTGAGCCTAGCAGGCTGTACGAATGTGAT
1 TTGGGCCTAATGGGCCATATGAATGTGAT
28357940 TTGGGCCTAATGGGCCATATGAATG
1 TTGGGCCTAATGGGCCATATGAATG
28357965 AAATGGGGTC
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (29 bp):
TTGGGCCTAATGGGCCATATGAATGTGAT
Found at i:28360030 original size:21 final size:20
Alignment explanation
Indices: 28360006--28360047 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
28359996 TCATTTTCAA
28360006 TCTCAATCT-TGTTTTGCTTTC
1 TCTCAATCTCT-TTTT-CTTTC
*
28360027 TCTCACTCTCTTTTTCTTTC
1 TCTCAATCTCTTTTTCTTTC
28360047 T
1 T
28360048 TTTCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 12 0.63
22 1 0.05
ACGTcount: A:0.07, C:0.29, G:0.05, T:0.60
Consensus pattern (20 bp):
TCTCAATCTCTTTTTCTTTC
Found at i:28366822 original size:136 final size:137
Alignment explanation
Indices: 28366645--28367203 Score: 761
Period size: 136 Copynumber: 4.0 Consensus size: 137
28366635 ACACAGATAA
* * *
28366645 AATTAATAAATGAATTTGATTCATATAAAAAATTAATTGTATATATTTTACTGAATTTATTAATA
1 AATT-ATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATTAATA
* * * **
28366710 TGAATAATTATATTAATAAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
65 TAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
*
28366775 AAAAATAT
130 AAGAATAT
28366783 AATTA-ATATGAATTTGATTCATACAAAATATTAATTGTATACT-TTTTACTGAATTTATTAATA
1 AATTATATATGAATTTGATTCATACAAAATATTAATTGTATA-TATTTTACTGAATTTATTAATA
* * ** *
28366846 TAAACAATTATATTAATTACTTTTGGTCAAAATATAAAATCCATGGAAATTAGTATTCTTTTGGA
65 TAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
28366911 AAGAATAT
130 AAGAATAT
* *
28366919 AATTAGTATATGAATTTAATTCATACAAAATATTATTTGTTTATATATTTTA-TCGAATTTATTA
1 AATTA-TATATGAATTTGATTCATACAAAATATTAATTG--TATATATTTTACT-GAATTTATTA
* *
28366983 ATATAAACAGTTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATACTTTT
62 ATATAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTC-TTT
28367048 TGGAAAGAATAT
126 TGGAAAGAATAT
* *
28367060 AATTAACATATATGAATTTTATTCATA-AAAATTATTAATTGTATATATTTTACTAAATTTATTA
1 AATT---ATATATGAATTTGATTCATACAAAA-TATTAATTGTATATATTTTACTGAATTTATTA
*
28367124 ATATAAA-AAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACAT-GATAATTAATATTCTT
62 ATATAAACAA-TTATATTAATTAATTTTGATCAAAATATAAAAGACATGGA-AATTAATATTCTT
*
28367187 TTAGAAAGAATAT
125 TTGGAAAGAATAT
28367200 AATT
1 AATT
28367204 CCTTTTTCTA
Statistics
Matches: 376, Mismatches: 30, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
136 120 0.32
137 2 0.01
138 34 0.09
139 2 0.01
140 94 0.25
141 92 0.24
142 5 0.01
143 26 0.07
144 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (137 bp):
AATTATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATTAATAT
AAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAA
AGAATAT
Found at i:28367186 original size:281 final size:274
Alignment explanation
Indices: 28366645--28367203 Score: 786
Period size: 281 Copynumber: 2.0 Consensus size: 274
28366635 ACACAGATAA
* *
28366645 AATTAATAAATGAATTTGATTCATATAAAAAATTAATTGTATATATTTTACTGAATTTATTAATA
1 AATTAATAAATGAATTTAATTCATACAAAAAATTAATTGTATATATTTTACTGAATTTATTAATA
* * *
28366710 TGAATAATTATATTAATAAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATAAATTTCAATCAAAATATAAAAGACATGGAAATTAATATACTTTTGGA
*
28366775 AAAAATATAATTAATATGAATTTGATTCATACAAAATATTAATTGTATACTTTTTACTGAATTTA
131 AAAAATATAATTAATATGAATTTGATTCATACAAAATATTAATTGTATACTTTTTACTAAATTTA
* ** *
28366840 TTAATATAAACAATTATATTAATTACTTTTGGTCAAAATATAAAATCCATGGAAATTAGTATTCT
196 TTAATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCT
*
28366905 TTTGGAAAGAATAT
261 TTTAGAAAGAATAT
* * * *
28366919 AATTAGTATATGAATTTAATTCATACAAAATATTATTTGTTTATATATTTTA-TCGAATTTATTA
1 AATTAATAAATGAATTTAATTCATACAAAAAATTAATTG--TATATATTTTACT-GAATTTATTA
* * **
28366983 ATATAAACAGTTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATACTTTT
63 ATATAAACAATTATATTAATAAATTTCAATCAAAATATAAAAGACATGGAAATTAATATAC-TTT
* *
28367048 TGGAAAGAATATAATTAACATATATGAATTTTATTCATA-AAAATTATTAATTGTATA-TATTTT
127 TGGAAAAAATATAATT---A-ATATGAATTTGATTCATACAAAA-TATTAATTGTATACT-TTTT
28367111 ACTAAATTTATTAATATAAA-AAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACAT-GAT
186 ACTAAATTTATTAATATAAACAA-TTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGA-
28367174 AATTAATATTCTTTTAGAAAGAATAT
249 AATTAATATTCTTTTAGAAAGAATAT
28367200 AATT
1 AATT
28367204 CCTTTTTCTA
Statistics
Matches: 252, Mismatches: 21, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
274 33 0.13
275 1 0.00
276 75 0.30
277 18 0.07
280 10 0.04
281 115 0.46
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (274 bp):
AATTAATAAATGAATTTAATTCATACAAAAAATTAATTGTATATATTTTACTGAATTTATTAATA
TAAACAATTATATTAATAAATTTCAATCAAAATATAAAAGACATGGAAATTAATATACTTTTGGA
AAAAATATAATTAATATGAATTTGATTCATACAAAATATTAATTGTATACTTTTTACTAAATTTA
TTAATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCT
TTTAGAAAGAATAT
Found at i:28367306 original size:75 final size:75
Alignment explanation
Indices: 28367179--28367325 Score: 213
Period size: 75 Copynumber: 2.0 Consensus size: 75
28367169 ATGATAATTA
* * * * * *
28367179 ATATTCTTTTAGAAAGAATATAATTCCTTTTTCTAACTTTTCATTTGTCTTCTCTGTTAATAAGG
1 ATATTATTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGA
28367244 GAATAATCTT
66 GAATAATCTT
* * *
28367254 ATATTATTTTGGAAAGAATATAATTTATTTTTCTAACTTTCCATTTGCCTTCTCTATTAGTAAGA
1 ATATTATTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGA
28367319 GAATAAT
66 GAATAAT
28367326 AATGGTTTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (75 bp):
ATATTATTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGA
GAATAATCTT
Found at i:28372199 original size:30 final size:30
Alignment explanation
Indices: 28372165--28372363 Score: 172
Period size: 30 Copynumber: 6.7 Consensus size: 30
28372155 AGCCAAAGCT
*
28372165 ATCCCTTTCCATTATTTGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* *
28372195 ATCCCTTTTCATT-GTTGATGGTCCTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* * * *
28372224 ATCCCTTTTCATAATTTGATAGCCG-AAGCTC
1 ATCCCTTTTCATTATTTGATGGTCGTCA-C-C
** * * *** *
28372255 -TCCCTTTTCACAATTCGATAG-CCAAAGTC
1 ATCCCTTTTCATTATTTGATGGTCGTCA-CC
* *
28372284 ATCCCTTTTCATTGTTCGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
28372314 ATCCCTTTTCATTATTTGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* *
28372344 ATCCTTTTTCATAATTTGAT
1 ATCCCTTTTCATTATTTGAT
28372364 AGCCTAGGCT
Statistics
Matches: 138, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
29 29 0.21
30 106 0.77
31 3 0.02
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATTATTTGATGGTCGTCACC
Found at i:28372350 original size:119 final size:120
Alignment explanation
Indices: 28372150--28372367 Score: 352
Period size: 119 Copynumber: 1.8 Consensus size: 120
28372140 TTTTCATAGC
*
28372150 TCGATAGCCAAAGCTATCCCTTTCCATTATTTGATGGTCGTCACCATCCCTTTTCATTGTTGATG
1 TCGATAGCCAAAGCTATCCCTTTCCATTATTCGATGGTCGTCACCATCCCTTTTCATTGTTGATG
28372215 GTCCTCACCATCCC-TTTTCATAATTTGATAGCCGAAGCTCTCCCTTTTCACAAT
66 GTCCTCACCATCCCTTTTTCATAATTTGATAGCCGAAGCTCTCCCTTTTCACAAT
* * *
28372269 TCGATAGCCAAAG-TCATCCCTTTTCATTGTTCGATGGTCGTCACCATCCCTTTTCATTATTTGA
1 TCGATAGCCAAAGCT-ATCCCTTTCCATTATTCGATGGTCGTCACCATCCCTTTTCATT-GTTGA
*
28372333 TGGTCGTCACCAT-CCTTTTTCATAATTTGATAGCC
64 TGGTCCTCACCATCCCTTTTTCATAATTTGATAGCC
28372368 TAGGCTATCC
Statistics
Matches: 91, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
118 1 0.01
119 55 0.60
120 35 0.38
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (120 bp):
TCGATAGCCAAAGCTATCCCTTTCCATTATTCGATGGTCGTCACCATCCCTTTTCATTGTTGATG
GTCCTCACCATCCCTTTTTCATAATTTGATAGCCGAAGCTCTCCCTTTTCACAAT
Found at i:28372394 original size:31 final size:31
Alignment explanation
Indices: 28372350--28372419 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
28372340 CACCATCCTT
* *
28372350 TTTCA-TAATTTGATAGCCTAGGCTATCCCA
1 TTTCATTAATTTGATAGCCGAAGCTATCCCA
* * **
28372380 TTTCATTATTTTGATTGCCGAAGCTATCCTT
1 TTTCATTAATTTGATAGCCGAAGCTATCCCA
28372411 TTTCATTAA
1 TTTCATTAA
28372420 CCGATGATCA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (31 bp):
TTTCATTAATTTGATAGCCGAAGCTATCCCA
Found at i:28373950 original size:6 final size:6
Alignment explanation
Indices: 28373939--28373969 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28373929 CGATTTTCTG
*
28373939 CTTCCC CTTCCC CTTTCC CTTCCC CTTCCC C
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC C
28373970 CATCCTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CTTCCC
Found at i:28377099 original size:19 final size:20
Alignment explanation
Indices: 28377075--28377116 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
28377065 CAAACACCAT
28377075 AAAAGTAAATCA-TTTCCAG
1 AAAAGTAAATCATTTTCCAG
28377094 AAAAGTAAATCATTTTCCAG
1 AAAAGTAAATCATTTTCCAG
28377114 AAA
1 AAA
28377117 TCATTTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAAGTAAATCATTTTCCAG
Found at i:28377119 original size:14 final size:14
Alignment explanation
Indices: 28377100--28377137 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
28377090 CCAGAAAAGT
28377100 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
28377114 AAATCATTTTCTAG
1 AAATCATTTTCCAG
*
28377128 AAAACATTTT
1 AAATCATTTT
28377138 ATTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:28386854 original size:46 final size:46
Alignment explanation
Indices: 28386802--28386977 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
28386792 TGGTTGAGCA
*
28386802 TCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
28386848 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
28386893 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
28386941 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28386978 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.58
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28386958 original size:93 final size:93
Alignment explanation
Indices: 28386799--28386969 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
28386789 GGATGGTTGA
* **
28386799 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28386864 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
28386892 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28386957 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
28386970 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28389776 original size:20 final size:20
Alignment explanation
Indices: 28389751--28389792 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
28389741 AAGTTGTAGG
*
28389751 TTTGCTTACCAAAAATGTTA
1 TTTGCTTACCAAAAACGTTA
28389771 TTTGCTTACCAAAAACGTTA
1 TTTGCTTACCAAAAACGTTA
28389791 TT
1 TT
28389793 ATTTTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTGCTTACCAAAAACGTTA
Found at i:28390156 original size:27 final size:26
Alignment explanation
Indices: 28390094--28390157 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 26
28390084 GAGCCCTATT
* *
28390094 CAATATCAGTACAGTTTGGCCTTAGCC
1 CAATA-CAGTACAGTGTGGCCTAAGCC
28390121 CTTAA-ACAGTAGCAGTGTGGCCTAAGCC
1 C--AATACAGTA-CAGTGTGGCCTAAGCC
28390149 CAATACAGT
1 CAATACAGT
28390158 TTCAGTATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
26 2 0.06
27 11 0.35
28 16 0.52
29 2 0.06
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (26 bp):
CAATACAGTACAGTGTGGCCTAAGCC
Found at i:28390594 original size:24 final size:24
Alignment explanation
Indices: 28390562--28390638 Score: 136
Period size: 24 Copynumber: 3.2 Consensus size: 24
28390552 AAGTCTGTCA
28390562 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
28390586 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
28390610 GGAGAGGATTTAGGAGCTAATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
28390634 GGAGA
1 GGAGA
28390639 ATAGTGTTGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.34, C:0.04, G:0.42, T:0.21
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:28392124 original size:27 final size:26
Alignment explanation
Indices: 28392049--28392156 Score: 110
Period size: 27 Copynumber: 4.0 Consensus size: 26
28392039 AAGCGTCCTA
* * *
28392049 GTGGCTATGCCACAATTATCTGATCTG
1 GTGGCTCTGTCAC-ATTATCTGTTCTG
*
28392076 GTGGCTCTG-CAACATAATTCTGTTCTG
1 GTGGCTCTGTC-ACATTA-TCTGTTCTG
*
28392103 GTGGCTCTGTCGCGATTATCTGTTCTG
1 GTGGCTCTGTCAC-ATTATCTGTTCTG
* *
28392130 GTGACTCTGTCACATTATTTGTTCTG
1 GTGGCTCTGTCACATTATCTGTTCTG
28392156 G
1 G
28392157 CAGCCATACT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
26 17 0.25
27 48 0.70
28 4 0.06
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (26 bp):
GTGGCTCTGTCACATTATCTGTTCTG
Found at i:28393770 original size:20 final size:21
Alignment explanation
Indices: 28393726--28393772 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
28393716 GGGCTTGCAC
28393726 GGCCCATCTGGGCCCAACACA
1 GGCCCATCTGGGCCCAACACA
*
28393747 -GCCCATTTGGGCCCAACA-A
1 GGCCCATCTGGGCCCAACACA
28393766 GGCCCAT
1 GGCCCAT
28393773 AACGGCACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.23, C:0.40, G:0.23, T:0.13
Consensus pattern (21 bp):
GGCCCATCTGGGCCCAACACA
Found at i:28398279 original size:11 final size:11
Alignment explanation
Indices: 28398263--28398287 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28398253 TCATACTGTA
28398263 AATAATAAAAT
1 AATAATAAAAT
28398274 AATAATAAAAT
1 AATAATAAAAT
28398285 AAT
1 AAT
28398288 TATTTTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:28409969 original size:22 final size:22
Alignment explanation
Indices: 28409944--28409993 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
28409934 TTTGGCGATG
*
28409944 TCATGAAAT-GAAGGAAGTGGCA
1 TCATGAAATAG-AGGAAGTGACA
**
28409966 TCATGACGTAGAGGAAGTGACA
1 TCATGAAATAGAGGAAGTGACA
28409988 TCATGA
1 TCATGA
28409994 TGTCGACCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (22 bp):
TCATGAAATAGAGGAAGTGACA
Found at i:28414886 original size:54 final size:54
Alignment explanation
Indices: 28414819--28414980 Score: 288
Period size: 54 Copynumber: 3.0 Consensus size: 54
28414809 GCTACAGGTA
* * *
28414819 TGTATGGAAAACTATTCAAGTATTGAACTAATGAAAGTTAAGAATTTCATTCTT
1 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
28414873 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
1 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
*
28414927 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTGAGAATTTCATACTT
1 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
28414981 ATTTAGTGAT
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (54 bp):
TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
Found at i:28425454 original size:20 final size:18
Alignment explanation
Indices: 28425421--28425457 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
28425411 TGTGATGTTG
28425421 ATATGATTAATTTAATTA
1 ATATGATTAATTTAATTA
28425439 ATATGACTTAAATTTAATT
1 ATATGA-TT-AATTTAATT
28425458 TGTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (18 bp):
ATATGATTAATTTAATTA
Found at i:28434023 original size:18 final size:18
Alignment explanation
Indices: 28434000--28434035 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28433990 AGTTTCATTC
28434000 TCGATACTTTGTGCACTA
1 TCGATACTTTGTGCACTA
28434018 TCGATACTTTGTGCACTA
1 TCGATACTTTGTGCACTA
28434036 AGTGTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (18 bp):
TCGATACTTTGTGCACTA
Found at i:28435382 original size:46 final size:45
Alignment explanation
Indices: 28435332--28435503 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 45
28435322 TGAGCATCCA
*
28435332 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAA-GTCCG
* *** * *
28435378 AACTCGTTGAGTTGAGTCCAACTTCGAGAGATGTAACTAG-GCA-TCCG
1 AACTCGTTGAGTTGAGTCCAAGTTC-ACTTATG-GA-T-GCGAAGTCCG
* * *
28435425 AGCTCATTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAA-GTCCG
* *
28435471 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCAAGTTCACTTATGG
28435504 GCGGGTTACA
Statistics
Matches: 101, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 61 0.60
47 30 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAAGTCCG
Found at i:28438280 original size:40 final size:40
Alignment explanation
Indices: 28438236--28438496 Score: 280
Period size: 40 Copynumber: 6.5 Consensus size: 40
28438226 GCTCGATTGT
* * *
28438236 CTTCGGGACATAGCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGACATAGCCCGGATT-TAGTAACTCGCACAAATGC
28438276 CTTCGGGA-ATTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGACA-TAGCCCGGATTTAGTAACTCGCACAAATGC
* * *
28438316 CTTCGGGACTTAACCC-GATTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAGCCCGGA-TTTAGTAACTCGCACAAATGC
* * * *
28438356 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAGCCCGGATTTAGTAACTCGCACAAATGC
* *
28438396 CTTCGGGA-ATTGACCCGGATTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAG-CCCGGATTTAGTAACTCGCACAAATGC
* * * *
28438436 CTTCGGGA-ATTGACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACATAG-CCCGGATTTAGTAAC-TCGCACAAATGC
*
28438477 CTTCGGGACTTAGCCCGGAT
1 CTTCGGGACATAGCCCGGAT
28438497 ACCATTCGAA
Statistics
Matches: 196, Mismatches: 17, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
39 4 0.02
40 162 0.83
41 28 0.14
42 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGACATAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:28438348 original size:80 final size:79
Alignment explanation
Indices: 28438264--28438493 Score: 318
Period size: 80 Copynumber: 2.9 Consensus size: 79
28438254 TTATAGTGAT
*
28438264 TCGCACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAA
1 TCGCACAAATGCCTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAA
28438329 CCCGATTTTGGTAAC
66 CCCGA-TTTGGTAAC
* * * * * *
28438344 TCGCACAAATGCCTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATTGA
1 TCGCACAAATGCCTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAA
28438409 CCCGGATTTGGTAAC
66 CCC-GATTTGGTAAC
* * *
28438424 TCGCACAAATGCCTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACTT
1 TCGCACAAATGCCTTCGGGAATTAG-CCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTT
*
28438488 AGCCCG
64 AACCCG
28438494 GATACCATTC
Statistics
Matches: 130, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
80 105 0.81
81 25 0.19
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (79 bp):
TCGCACAAATGCCTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAA
CCCGATTTGGTAAC
Found at i:28438435 original size:120 final size:121
Alignment explanation
Indices: 28438236--28438494 Score: 353
Period size: 120 Copynumber: 2.1 Consensus size: 121
28438226 GCTCGATTGT
* * * *
28438236 CTTCGGGACATAGCCCGGTTATAGTGATTCGCACAATTGCCTTCGGGAATTAGCCCGGATTTAGT
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTAGCCCGGATTTAGT
* * * *
28438301 AACTCGCACAAATGCCTTCGGGACTTAACCC-GATTTTGGTAAC-TCGCACAAATGC
66 AACTCGCACAAATGCCTTCGGGAATTAACCCGGA-TTTAGTAACTTAGCACAAAAGC
* * * *
28438356 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATT-GACCCGGATTTGG
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTAG-CCCGGATTTAG
* *
28438420 TAACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGTCACTTAGCACAAAAGC
65 TAACTCGCACAAATGCCTTCGGGAATTAACCCGGATTTAGTAACTTAGCACAAAAGC
28438477 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
28438495 ATACCATTCG
Statistics
Matches: 121, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
119 1 0.01
120 91 0.75
121 29 0.24
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (121 bp):
CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTAGCCCGGATTTAGT
AACTCGCACAAATGCCTTCGGGAATTAACCCGGATTTAGTAACTTAGCACAAAAGC
Found at i:28446405 original size:40 final size:39
Alignment explanation
Indices: 28446361--28446568 Score: 222
Period size: 40 Copynumber: 5.2 Consensus size: 39
28446351 GCTCGATTGT
* * * * *
28446361 CTTCGGGACATAGCCCAGTTATAGTGATTCGCACAATTGC
1 CTTCGGGACATAGCCCGGTT-TGGTAACTCGCACAAATGC
*
28446401 CTTCGGGA-ATTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGACA-TAGCCCGG-TTTGGTAACTCGCACAAATGC
* *
28446441 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAGCCCGG-TTTGGTAACTCGCACAAATGC
* **
28446481 CTTCGGGACTTAATCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAGCCCGG-TTTGGTAACTCGCACAAATGC
* *
28446521 CTTCGGGA-ATTGACCCAGATTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAG-CCC-GGTTTGGTAACTCGCACAAATGC
28446561 CTTCGGGA
1 CTTCGGGA
28446569 ATTCACCCGG
Statistics
Matches: 149, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
39 2 0.01
40 144 0.97
41 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (39 bp):
CTTCGGGACATAGCCCGGTTTGGTAACTCGCACAAATGC
Found at i:28446531 original size:120 final size:121
Alignment explanation
Indices: 28446389--28446613 Score: 328
Period size: 120 Copynumber: 1.9 Consensus size: 121
28446379 TTATAGTGAT
* * *
28446389 TCGCACAATTGCCTTCGGGAATT-AGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTA
1 TCGCACAAATGCCTTCGGGAATTGA-CCCAGATTTAGTAACTCGCACAAATGCCTTCGGGAATTA
* * * * *
28446453 ACCCGGTTTTGGTAAC-TCGCACAAATGCCTTCGGGACTTAATCCGGTTTTGGTAAC
65 ACCCGGATTTAGTAACTTAGCACAAAAGCCTTCGAGACTTAATCCGGTTTTGGTAAC
* *
28446509 TCGCACAAATGCCTTCGGGAATTGACCCAGATTTGGTAACTCGCACAAATGCCTTCGGGAATTCA
1 TCGCACAAATGCCTTCGGGAATTGACCCAGATTTAGTAACTCGCACAAATGCCTTCGGGAATTAA
*
28446574 CCCGGATTTAGTCACTTAGCACAAAAGCCTTCGAGACTTA
66 CCCGGATTTAGTAACTTAGCACAAAAGCCTTCGAGACTTA
28446614 GCCCGGATAC
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
120 70 0.76
121 22 0.24
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (121 bp):
TCGCACAAATGCCTTCGGGAATTGACCCAGATTTAGTAACTCGCACAAATGCCTTCGGGAATTAA
CCCGGATTTAGTAACTTAGCACAAAAGCCTTCGAGACTTAATCCGGTTTTGGTAAC
Found at i:28446569 original size:40 final size:40
Alignment explanation
Indices: 28446389--28446621 Score: 295
Period size: 40 Copynumber: 5.8 Consensus size: 40
28446379 TTATAGTGAT
* * *
28446389 TCGCACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAAC
1 TCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAAC
* *
28446429 TCGCACAAATGCCTTCGGGACTTAACCCGGTTTTGGTAAC
1 TCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAAC
* * *
28446469 TCGCACAAATGCCTTCGGGACTTAATCCGGTTTTGGTAAC
1 TCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAAC
* *
28446509 TCGCACAAATGCCTTCGGGAATTGACCCAGATTTGGTAAC
1 TCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAAC
* * *
28446549 TCGCACAAATGCCTTCGGGAATTCACCCGGATTTAGTCAC
1 TCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAAC
* * * * *
28446589 TTAGCACAAAAGCCTTCGAGACTTAGCCCGGAT
1 -TCGCACAAATGCCTTCGGGAATTAACCCGGAT
28446622 ACCATTCGAA
Statistics
Matches: 171, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
40 145 0.85
41 26 0.15
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
TCGCACAAATGCCTTCGGGAATTAACCCGGATTTGGTAAC
Found at i:28449906 original size:15 final size:15
Alignment explanation
Indices: 28449867--28449946 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
28449857 GTATCTTGGG
*
28449867 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
28449882 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
28449897 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
28449912 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
28449927 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
28449941 TTTCTT
1 TTTCTT
28449947 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:28449936 original size:30 final size:30
Alignment explanation
Indices: 28449858--28449945 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
28449848 CATAGTATCG
* * *
28449858 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
28449888 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
28449918 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
28449946 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:28454147 original size:39 final size:39
Alignment explanation
Indices: 28454093--28454236 Score: 243
Period size: 39 Copynumber: 3.7 Consensus size: 39
28454083 GAATGTTCGA
28454093 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
28454132 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28454171 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28454210 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
28454237 CTTTGTGCGG
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 88 0.91
40 9 0.09
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:28454183 original size:78 final size:79
Alignment explanation
Indices: 28454094--28454276 Score: 278
Period size: 78 Copynumber: 2.3 Consensus size: 79
28454084 AATGTTCGAG
28454094 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
28454158 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
28454172 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
28454237 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
28454251 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
28454277 GTTTGAACGA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
78 54 0.57
79 32 0.34
80 9 0.09
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:28460587 original size:40 final size:40
Alignment explanation
Indices: 28460521--28460664 Score: 150
Period size: 40 Copynumber: 3.6 Consensus size: 40
28460511 AAATTGAATG
* * *
28460521 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
28460560 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
28460600 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
*
28460640 CTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
28460665 TTCGTGCACG
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 16 0.19
40 69 0.81
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:28460685 original size:40 final size:40
Alignment explanation
Indices: 28460558--28460687 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
28460548 ATGCTGGAAA
* *
28460558 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
28460598 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
28460638 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
28460678 TTATATCCGG
1 TTATATCCGG
28460688 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:28468611 original size:40 final size:40
Alignment explanation
Indices: 28468545--28468688 Score: 150
Period size: 40 Copynumber: 3.6 Consensus size: 40
28468535 AAATTGAATG
* * *
28468545 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
28468584 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
28468624 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
*
28468664 CTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
28468689 TTCGTGCACG
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 16 0.19
40 69 0.81
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:28468709 original size:40 final size:40
Alignment explanation
Indices: 28468582--28468711 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
28468572 ATGCTGGAAA
* *
28468582 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
28468622 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
28468662 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
28468702 TTATATCCGG
1 TTATATCCGG
28468712 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:28473328 original size:44 final size:44
Alignment explanation
Indices: 28473217--28473341 Score: 214
Period size: 47 Copynumber: 2.8 Consensus size: 44
28473207 GCATCCATAA
28473217 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATC
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATC
*
28473261 TCACGAACTCGGACTCAACTCAACGAGTTCGAATGCCTAGTTACATC
1 T---GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATC
28473308 TGAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCC
28473342 CAAATATCCC
Statistics
Matches: 76, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
44 33 0.43
47 43 0.57
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (44 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATC
Found at i:28475311 original size:30 final size:30
Alignment explanation
Indices: 28475267--28475355 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
28475257 CAAAGATAAC
28475267 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
28475296 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
28475326 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
28475356 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:28475315 original size:15 final size:15
Alignment explanation
Indices: 28475267--28475346 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
28475257 CAAAGATAAC
*
28475267 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
28475281 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
28475296 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
28475311 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
28475326 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
28475341 AAGAAA
1 AAGAAA
28475347 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:28475355 original size:15 final size:15
Alignment explanation
Indices: 28475278--28475355 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
28475268 AGAAAACCGA
28475278 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
28475293 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
28475307 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
28475322 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
28475338 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
28475353 ATA
1 ATA
28475356 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:28478417 original size:47 final size:47
Alignment explanation
Indices: 28478349--28478475 Score: 245
Period size: 47 Copynumber: 2.7 Consensus size: 47
28478339 ATCCATAAAT
28478349 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
*
28478396 GAACTCGGACTCAACTCAACGAGTTCGAATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
28478443 GAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC
28478476 CAAATATCCC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
47 78 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:28486877 original size:3 final size:3
Alignment explanation
Indices: 28486869--28486926 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
28486859 TTGGATGTTT
28486869 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28486917 TTA TTA TTA T
1 TTA TTA TTA T
28486927 GTTAGTTTAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28489429 original size:20 final size:20
Alignment explanation
Indices: 28489399--28489462 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
28489389 CTGTTTTGTT
28489399 ATGGG-CCAACTGTATTGAA
1 ATGGGCCCAACTGTATTGAA
28489418 ATGGGCCCAACTGTATTGAA
1 ATGGGCCCAACTGTATTGAA
* *
28489438 ATGGGCCCAACTGTGTTGAT
1 ATGGGCCCAACTGTATTGAA
28489458 ATGGG
1 ATGGG
28489463 TTAAGGCCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
19 5 0.12
20 37 0.88
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTGAA
Found at i:28491304 original size:3 final size:3
Alignment explanation
Indices: 28491296--28491333 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
28491286 AATTTGGATG
28491296 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28491334 TAGTATGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28493832 original size:20 final size:20
Alignment explanation
Indices: 28493807--28493844 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28493797 TTGTTATGGG
28493807 CCAACTGTATTGAAATGGTC
1 CCAACTGTATTGAAATGGTC
*
28493827 CCAACTGTATTGATATGG
1 CCAACTGTATTGAAATGG
28493845 GTTAAGGCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (20 bp):
CCAACTGTATTGAAATGGTC
Found at i:28496343 original size:13 final size:13
Alignment explanation
Indices: 28496325--28496350 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28496315 GCGTGTGGGC
28496325 CCACACAAGCATG
1 CCACACAAGCATG
28496338 CCACACAAGCATG
1 CCACACAAGCATG
28496351 TGGGTTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.08
Consensus pattern (13 bp):
CCACACAAGCATG
Found at i:28498060 original size:24 final size:24
Alignment explanation
Indices: 28498007--28498067 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
28497997 CCAGGTAGGT
* ***
28498007 ACAAAGCCCGATAAACACACTGGC
1 ACAAAGCCTGATAAACACACCAAC
*
28498031 AAAAAGCCTGATAAACACACCAAC
1 ACAAAGCCTGATAAACACACCAAC
28498055 ACAAAGCCTGATA
1 ACAAAGCCTGATA
28498068 GATAACACTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.48, C:0.30, G:0.13, T:0.10
Consensus pattern (24 bp):
ACAAAGCCTGATAAACACACCAAC
Found at i:28499408 original size:40 final size:40
Alignment explanation
Indices: 28499353--28499562 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
28499343 AACATTGGAA
28499353 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28499393 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28499433 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
28499473 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
28499512 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
28499553 CTATATCCGG
1 ATATATCCGG
28499563 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:28506626 original size:40 final size:40
Alignment explanation
Indices: 28506571--28506780 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
28506561 AACATTGGAA
28506571 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28506611 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28506651 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
28506691 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
28506730 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
28506771 CTATATCCGG
1 ATATATCCGG
28506781 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:28518089 original size:40 final size:40
Alignment explanation
Indices: 28518012--28518273 Score: 420
Period size: 40 Copynumber: 6.6 Consensus size: 40
28518002 AAACCAAGTA
* * *
28518012 CCTTCGGGAATTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
28518051 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
28518091 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
28518131 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
28518171 CCTTTGAGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
28518211 CCTTCGGGACTTAGCCCGGTTATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
28518251 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
28518274 CATCCGAATA
Statistics
Matches: 210, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
39 14 0.07
40 196 0.93
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:28521475 original size:79 final size:82
Alignment explanation
Indices: 28521359--28521543 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
28521349 ACGACTCGCT
** * *
28521359 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
28521422 GGGTTTAGTAACTT-GCA
65 GGATATAGTAACTTAGCA
* **
28521439 CAAATGCCTTCGGG-CTTAGCCCGGATT-TATTAACTCGCACGAATGCCTTCGGATCCTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACGAATGCCTTCGGATCCTAACCCG
*
28521502 GATATAGTCACTTAGCA
66 GATATAGTAACTTAGCA
28521519 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28521544 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACGAATGCCTTCGGATCCTAACCCG
GATATAGTAACTTAGCA
Found at i:28521543 original size:40 final size:39
Alignment explanation
Indices: 28521352--28521543 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
28521342 GGATATAACG
* ** * *
28521352 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
28521392 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
28521432 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
28521471 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
28521511 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
28521544 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:28529508 original size:79 final size:81
Alignment explanation
Indices: 28529407--28529591 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
28529397 ACGACTCGCT
** * *
28529407 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
28529470 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
28529487 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
28529551 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
28529567 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28529592 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:28529591 original size:40 final size:39
Alignment explanation
Indices: 28529400--28529591 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
28529390 GGATATAACG
* ** * *
28529400 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
28529440 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
28529480 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
28529519 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
28529559 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
28529592 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:28547005 original size:33 final size:33
Alignment explanation
Indices: 28546968--28547035 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
28546958 ATTGAACAAT
*
28546968 TGGGATAAGTAAAGTTGTTCAAAATCCATAGAA
1 TGGGATAAGTAAAGTTATTCAAAATCCATAGAA
28547001 TGGGATAAGTAAAGTTATTCAAAATCCATAGAA
1 TGGGATAAGTAAAGTTATTCAAAATCCATAGAA
28547034 TG
1 TG
28547036 CATGCATAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (33 bp):
TGGGATAAGTAAAGTTATTCAAAATCCATAGAA
Found at i:28547937 original size:15 final size:15
Alignment explanation
Indices: 28547917--28547961 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
28547907 TATTGTATTT
28547917 TGGATTTCTTTATCA
1 TGGATTTCTTTATCA
* *
28547932 TGGATTTCTTTGTCT
1 TGGATTTCTTTATCA
*
28547947 TAGGACTTCTTTATC
1 T-GGATTTCTTTATC
28547962 TTGGTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (15 bp):
TGGATTTCTTTATCA
Found at i:28550517 original size:14 final size:16
Alignment explanation
Indices: 28550498--28550536 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
28550488 AAGAAAATGA
*
28550498 TGATATATGACA-A-G
1 TGATATATGAAATAGG
28550512 TGATATATGAAATAGG
1 TGATATATGAAATAGG
28550528 TGATATATG
1 TGATATATG
28550537 TTATGTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 1 0.05
16 10 0.45
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (16 bp):
TGATATATGAAATAGG
Found at i:28553879 original size:29 final size:29
Alignment explanation
Indices: 28553837--28553895 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28553827 AATAGGTGAG
28553837 TATTACATAGTGCATTAATTCACATCACA
1 TATTACATAGTGCATTAATTCACATCACA
28553866 TATTACATAGTGCATTAATTCACATCACA
1 TATTACATAGTGCATTAATTCACATCACA
28553895 T
1 T
28553896 TCTCAGTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (29 bp):
TATTACATAGTGCATTAATTCACATCACA
Found at i:28556850 original size:26 final size:26
Alignment explanation
Indices: 28556817--28556866 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
28556807 GGTGCATGGG
* *
28556817 TGATAAAATAATGAAAA-AAAAAATA
1 TGATAAAACAAAGAAAAGAAAAAATA
28556842 TGATGAAAACAAAGAAAAGAAAAAA
1 TGAT-AAAACAAAGAAAAGAAAAAA
28556867 AAAAGTGTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 11 0.52
27 6 0.29
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (26 bp):
TGATAAAACAAAGAAAAGAAAAAATA
Found at i:28557977 original size:31 final size:28
Alignment explanation
Indices: 28557939--28558038 Score: 103
Period size: 27 Copynumber: 3.5 Consensus size: 28
28557929 CATGAAATTG
*
28557939 GCACTAAGTGTGCGGGTTTAAAATTTGTACA
1 GCACTAAGTGTGCGAGTTT--AATTT-TACA
* * *
28557970 GCACTAAGTATGCGAGTTTGATTTTATA
1 GCACTAAGTGTGCGAGTTTAATTTTACA
* * *
28557998 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTAATTTTACA
28558025 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28558039 GACTCACTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
27 24 0.38
28 18 0.29
29 4 0.06
31 17 0.27
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTTTACA
Found at i:28558025 original size:27 final size:28
Alignment explanation
Indices: 28557969--28558038 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
28557959 AAATTTGTAC
* *
28557969 AGCACTAAGTATGCGAGTTTGATTTTAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
28557997 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
28558024 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
28558039 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 24 0.60
28 16 0.40
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:28558049 original size:27 final size:27
Alignment explanation
Indices: 28557994--28558050 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
28557984 AGTTTGATTT
* * *
28557994 TATAGCACTAAGTGTGCGAGTTGATTA
1 TATAGCACTAAGTGTGCGAGCTCACTA
28558021 TATAGCACTAAGTGTGCG-GACTCACTA
1 TATAGCACTAAGTGTGCGAG-CTCACTA
28558048 TAT
1 TAT
28558051 GTTTTGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (27 bp):
TATAGCACTAAGTGTGCGAGCTCACTA
Found at i:28560942 original size:29 final size:29
Alignment explanation
Indices: 28560908--28561040 Score: 97
Period size: 29 Copynumber: 4.6 Consensus size: 29
28560898 TACTCGATTT
* *
28560908 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATGCCATTCAAGCC
* * * *
28560937 CGCACACATAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATGCCATTCAAGCC
** * *
28560966 CGCACACTTAGTGCCAT-ATATTTCCAGCA
1 CGCACACTTAGTGCCATGCCA-TTCAAGCC
* **** * *
28560995 TGCACACTTAGTGCCATATTTTTCCAGCA
1 CGCACACTTAGTGCCATGCCATTCAAGCC
28561024 CGCACACTTAGTGCCAT
1 CGCACACTTAGTGCCAT
28561041 ATTGTCACCG
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
29 85 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCCATTCAAGCC
Found at i:28561000 original size:58 final size:57
Alignment explanation
Indices: 28560907--28561042 Score: 146
Period size: 58 Copynumber: 2.4 Consensus size: 57
28560897 ATACTCGATT
** * * *
28560907 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACATAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCAT-ATATTTAAGCACGCACACATAGTGCCATACCCTTCCAGC
* * * ***
28560965 TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATTTTTCCAGC
1 TCGCACACTTAGTGCCATATATTT-AAGCACGCACACATAGTGCCATACCCTTCCAGC
*
28561023 ACGCACACTTAGTGCCATAT
1 TCGCACACTTAGTGCCATAT
28561043 TGTCACCGTA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
57 4 0.06
58 61 0.94
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (57 bp):
TCGCACACTTAGTGCCATATATTTAAGCACGCACACATAGTGCCATACCCTTCCAGC
Found at i:28561041 original size:29 final size:29
Alignment explanation
Indices: 28560966--28561043 Score: 138
Period size: 29 Copynumber: 2.7 Consensus size: 29
28560956 CCTTCGAGCT
*
28560966 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATTTTTCCAGCA
*
28560995 TGCACACTTAGTGCCATATTTTTCCAGCA
1 CGCACACTTAGTGCCATATTTTTCCAGCA
28561024 CGCACACTTAGTGCCATATT
1 CGCACACTTAGTGCCATATT
28561044 GTCACCGTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATTTTTCCAGCA
Found at i:28568730 original size:29 final size:28
Alignment explanation
Indices: 28568697--28568769 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
28568687 CCTTCGAGCT
28568697 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATAT-TTTCCAGCA
*
28568726 TGCACACTTAGTGCCATATTTTCCAGCA
1 CGCACACTTAGTGCCATATTTTCCAGCA
28568754 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
28568770 ATCTCGTCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
28 24 0.57
29 18 0.43
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATTTTCCAGCA
Found at i:28568758 original size:28 final size:29
Alignment explanation
Indices: 28568639--28568769 Score: 131
Period size: 29 Copynumber: 4.6 Consensus size: 29
28568629 TACTCGATTT
** * *
28568639 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* **** * *
28568668 CGCACACATAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
28568697 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
28568726 TGCACACTTAGTGCCATAT-TTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
28568754 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
28568770 ATCTCGTCAC
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
28 26 0.31
29 59 0.69
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:28571853 original size:40 final size:40
Alignment explanation
Indices: 28571808--28571937 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
28571798 CGGAATATAA
28571808 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
28571848 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
28571888 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
28571928 CCGGATATAA
1 CCGGATATAA
28571938 TTTCCAGCAT
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 73 0.99
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:28571952 original size:40 final size:40
Alignment explanation
Indices: 28571808--28571973 Score: 133
Period size: 40 Copynumber: 4.2 Consensus size: 40
28571798 CGGAATATAA
* ** * *
28571808 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAAC
* * *
28571848 CCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-CAGCAC-AATTGCCTTCGGGTCTTAAC
* ** *
28571888 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAAC
** * * *
28571928 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTT-AG
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAAC
28571966 CCGGATAT
1 CCGGATAT
28571974 CATTCAATTT
Statistics
Matches: 102, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
38 9 0.09
39 5 0.05
40 86 0.84
41 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAAC
Found at i:28579863 original size:40 final size:40
Alignment explanation
Indices: 28579818--28579985 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
28579808 CGGAATATAA
28579818 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
28579858 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
28579898 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
28579938 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
28579978 CCGGATAT
1 CCGGATAT
28579986 CATTCAATTT
Statistics
Matches: 104, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 103 0.99
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:28579968 original size:80 final size:80
Alignment explanation
Indices: 28579834--28579983 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
28579824 ATAACCACGT
* *
28579834 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
28579899 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * ** * *
28579914 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
28579977 CCCGGAT
64 CCCGGAT
28579984 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 3 0.05
80 57 0.95
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:28583371 original size:30 final size:30
Alignment explanation
Indices: 28583335--28583401 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
28583325 TTGTAACCAT
**
28583335 TCTTTTTCTCTCTCAAACTCTTTTTCATTC
1 TCTTTTTCAATCTCAAACTCTTTTTCATTC
*** *
28583365 TCTTTTTCAATCTCATTTTCTTTTTCATTT
1 TCTTTTTCAATCTCAAACTCTTTTTCATTC
28583395 TCTTTTT
1 TCTTTTT
28583402 GTTTTTCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (30 bp):
TCTTTTTCAATCTCAAACTCTTTTTCATTC
Found at i:28583401 original size:18 final size:18
Alignment explanation
Indices: 28583359--28583410 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
28583349 AAACTCTTTT
*
28583359 TCATTCTCTTTTTCAATC
1 TCATTTTCTTTTTCAATC
* *
28583377 TCATTTTCTTTTTCATTT
1 TCATTTTCTTTTTCAATC
* *
28583395 TCTTTTTGTTTTTCAA
1 TCATTTTCTTTTTCAA
28583411 AGGCTTTATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.19, G:0.02, T:0.65
Consensus pattern (18 bp):
TCATTTTCTTTTTCAATC
Found at i:28583408 original size:12 final size:12
Alignment explanation
Indices: 28583377--28583401 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28583367 TTTTTCAATC
28583377 TCATTTTCTTTT
1 TCATTTTCTTTT
28583389 TCATTTTCTTTT
1 TCATTTTCTTTT
28583401 T
1 T
28583402 GTTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:28583480 original size:5 final size:5
Alignment explanation
Indices: 28583470--28583527 Score: 52
Period size: 5 Copynumber: 12.0 Consensus size: 5
28583460 CTTTTGCCTC
* *
28583470 TCTTT TCTTT TTTTT TCGTTT TCTTT T-TCT TCTTT T-TCTT T-TTT T-TTT
1 TCTTT TCTTT TCTTT TC-TTT TCTTT TCTTT TCTTT TCT-TT TCTTT TCTTT
28583518 TCTTT TCTTT
1 TCTTT TCTTT
28583528 GTTTTCTCGT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 11 0.24
5 29 0.64
6 5 0.11
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:28583499 original size:6 final size:6
Alignment explanation
Indices: 28583472--28583527 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
28583462 TTTGCCTCTC
* *
28583472 TTTTC- TTTT-T TTTTCG TTTTCT TTTTC- --TTCT TTTTCT TTTTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
28583515 TTTTC- TTTTCT TT
1 TTTTCT TTTTCT TT
28583528 GTTTTCTCGT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
3 3 0.07
5 13 0.32
6 25 0.61
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:28583532 original size:9 final size:8
Alignment explanation
Indices: 28583472--28583534 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 8
28583462 TTTGCCTCTC
28583472 TTTTCTTT
1 TTTTCTTT
*
28583480 TTTT-TTCG
1 TTTTCTT-T
28583488 TTTTCTTT
1 TTTTCTTT
28583496 TTCTTCTTT
1 TT-TTCTTT
28583505 TTCTT-TTT
1 TT-TTCTTT
*
28583513 TTTT-TTC
1 TTTTCTTT
28583520 TTTTCTTT
1 TTTTCTTT
28583528 GTTTTCT
1 -TTTTCT
28583535 CGTTACAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
7 10 0.22
8 17 0.37
9 19 0.41
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (8 bp):
TTTTCTTT
Found at i:28583532 original size:21 final size:22
Alignment explanation
Indices: 28583472--28583523 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
28583462 TTTGCCTCTC
*
28583472 TTTTCTTTTTTTTTCGTTTTCT
1 TTTTCTTTTTTTCTCGTTTTCT
*
28583494 TTTTCTTCTTTTTCT--TTTTTT
1 TTTTCTT-TTTTTCTCGTTTTCT
28583515 TTTTCTTTT
1 TTTTCTTTT
28583524 CTTTGTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 12 0.44
22 7 0.26
23 6 0.22
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (22 bp):
TTTTCTTTTTTTCTCGTTTTCT
Found at i:28594880 original size:15 final size:15
Alignment explanation
Indices: 28594862--28594898 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
28594852 GTTAATAAAT
28594862 AAAAAATATATAAT-
1 AAAAAATATATAATG
28594876 -AAAAATATATAATG
1 AAAAAATATATAATG
28594890 TAAAAAATA
1 -AAAAAATA
28594899 GGCAATAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.65
16 7 0.35
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AAAAAATATATAATG
Found at i:28594881 original size:13 final size:13
Alignment explanation
Indices: 28594863--28594888 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28594853 TTAATAAATA
28594863 AAAAATATATAAT
1 AAAAATATATAAT
28594876 AAAAATATATAAT
1 AAAAATATATAAT
28594889 GTAAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATATATAAT
Found at i:28598964 original size:43 final size:42
Alignment explanation
Indices: 28598878--28598991 Score: 106
Period size: 43 Copynumber: 2.7 Consensus size: 42
28598868 CATTAACTCA
* * *
28598878 TGATTTATGTGTAAGACCATGTTTGGGACATCGACATCGTATT
1 TGATTT-TGTGTAAGACCCTGTCTGGGACATCGACATCATATT
* *
28598921 TGATTTTGTGTAAGACCCTGTCTGGGATAGT-GGCATCAATATT
1 TGATTTTGTGTAAGACCCTGTCTGGGACA-TCGACATC-ATATT
***
28598964 TGATTACATGTAAGACCAC-GTCTGGGAC
1 TGATTTTGTGTAAGACC-CTGTCTGGGAC
28598992 GTTGGCATTG
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
42 25 0.42
43 33 0.56
44 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (42 bp):
TGATTTTGTGTAAGACCCTGTCTGGGACATCGACATCATATT
Found at i:28603961 original size:18 final size:18
Alignment explanation
Indices: 28603921--28603961 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28603911 AGGCCATTTT
28603921 TGGGCTTCGTGGGCCATA
1 TGGGCTTCGTGGGCCATA
*
28603939 CGGGCTT-GTGGGCCCATA
1 TGGGCTTCGTGGG-CCATA
28603957 TGGGC
1 TGGGC
28603962 CACATTATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.10, C:0.24, G:0.41, T:0.24
Consensus pattern (18 bp):
TGGGCTTCGTGGGCCATA
Found at i:28604129 original size:54 final size:54
Alignment explanation
Indices: 28604065--28604194 Score: 152
Period size: 54 Copynumber: 2.4 Consensus size: 54
28604055 CGTACCTGAA
* * ** * *
28604065 CCCTCATGTGATATAATGACGATTGTACCTTTATGTCATAAAATAACGATTTTG
1 CCCTTATGTGATAAAATGACGATTGTACCTGCACGTCATAAAATAACAATTTTG
* * * * *
28604119 CCCTTATGTGATAAAATGATGATTTTGCCTGCACGTGATAAAATGACAATTTTG
1 CCCTTATGTGATAAAATGACGATTGTACCTGCACGTCATAAAATAACAATTTTG
*
28604173 CCCTTATGTGATAAAATAACGA
1 CCCTTATGTGATAAAATGACGA
28604195 CTTATACCCT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (54 bp):
CCCTTATGTGATAAAATGACGATTGTACCTGCACGTCATAAAATAACAATTTTG
Found at i:28604142 original size:27 final size:27
Alignment explanation
Indices: 28604065--28604220 Score: 136
Period size: 27 Copynumber: 5.7 Consensus size: 27
28604055 CGTACCTGAA
* * * *
28604065 CCCTCATGTGATATAATGACGATTGTA
1 CCCTTATGTGATAAAATGACGATTTTG
* * *
28604092 CCTTTATGTCATAAAATAACGATTTTG
1 CCCTTATGTGATAAAATGACGATTTTG
*
28604119 CCCTTATGTGATAAAATGATGATTTTG
1 CCCTTATGTGATAAAATGACGATTTTG
* * *
28604146 -CCTGCACGTGATAAAATGACAATTTTG
1 CCCT-TATGTGATAAAATGACGATTTTG
* * *
28604173 CCCTTATGTGATAAAATAACGACTTATA
1 CCCTTATGTGATAAAATGACGA-TTTTG
*
28604201 CCCTCATAG-GATAAAATGAC
1 CCCTTAT-GTGATAAAATGAC
28604221 CGAAATACCC
Statistics
Matches: 102, Mismatches: 23, Indels: 7
0.77 0.17 0.05
Matches are distributed among these distances:
26 3 0.03
27 76 0.75
28 22 0.22
29 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (27 bp):
CCCTTATGTGATAAAATGACGATTTTG
Found at i:28604235 original size:27 final size:27
Alignment explanation
Indices: 28604198--28604328 Score: 149
Period size: 27 Copynumber: 4.9 Consensus size: 27
28604188 ATAACGACTT
28604198 ATACCCTCATAGGATAAAATGACCGAA
1 ATACCCTCATAGGATAAAATGACCGAA
* * * *
28604225 ATACCCCCATAGGGTAGAAGGACCGAA
1 ATACCCTCATAGGATAAAATGACCGAA
28604252 ATACCCTCATAGGATAAAATGACCGAA
1 ATACCCTCATAGGATAAAATGACCGAA
* * *
28604279 ATA-CCTCCAAATGG-TAGAATGATCGAA
1 ATACCCT-CATA-GGATAAAATGACCGAA
* *
28604306 ATACCCTTATAGGGTAAAATGAC
1 ATACCCTCATAGGATAAAATGAC
28604329 TACAATACCC
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
26 5 0.06
27 75 0.88
28 5 0.06
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.19
Consensus pattern (27 bp):
ATACCCTCATAGGATAAAATGACCGAA
Found at i:28604337 original size:54 final size:54
Alignment explanation
Indices: 28604198--28604328 Score: 199
Period size: 54 Copynumber: 2.4 Consensus size: 54
28604188 ATAACGACTT
*
28604198 ATACCCTCATAGGATAAAATGACCGAAATACCCCCATAGGGTAGAAGGACCGAA
1 ATACCCTCATAGGATAAAATGACCGAAATACCCCCAAAGGGTAGAAGGACCGAA
* * * *
28604252 ATACCCTCATAGGATAAAATGACCGAAATACCTCCAAATGGTAGAATGATCGAA
1 ATACCCTCATAGGATAAAATGACCGAAATACCCCCAAAGGGTAGAAGGACCGAA
* *
28604306 ATACCCTTATAGGGTAAAATGAC
1 ATACCCTCATAGGATAAAATGAC
28604329 TACAATACCC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.19
Consensus pattern (54 bp):
ATACCCTCATAGGATAAAATGACCGAAATACCCCCAAAGGGTAGAAGGACCGAA
Found at i:28604789 original size:34 final size:34
Alignment explanation
Indices: 28604751--28604825 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
28604741 CTGATTATTA
28604751 TTACTGAAACGGGCTAAAGCCCAGACTTG-TACTG
1 TTACTGAAACGGGCTAAAGCCCAGAC-TGCTACTG
* * * *
28604785 TTACTAAAATGGGCTAAGGCCTAGACTGCTACTG
1 TTACTGAAACGGGCTAAAGCCCAGACTGCTACTG
28604819 TTACTGA
1 TTACTGA
28604826 TATGCTTAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 2 0.06
34 33 0.94
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (34 bp):
TTACTGAAACGGGCTAAAGCCCAGACTGCTACTG
Found at i:28608410 original size:27 final size:27
Alignment explanation
Indices: 28608380--28608433 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
28608370 ATGACCAAAA
*
28608380 TACCCCTATAGGGTAAAATGACT-ATTT
1 TACCCCTAGAGGG-AAAATGACTGATTT
*
28608407 TACCCCTCGAGGGAAAATGACTGATTT
1 TACCCCTAGAGGGAAAATGACTGATTT
28608434 GTGCTATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (27 bp):
TACCCCTAGAGGGAAAATGACTGATTT
Found at i:28608713 original size:20 final size:20
Alignment explanation
Indices: 28608697--28608828 Score: 192
Period size: 20 Copynumber: 6.6 Consensus size: 20
28608687 CGATATTTAA
28608697 GGCTTTGTGCCACTATTGAT
1 GGCTTTGTGCCACTATTGAT
*
28608717 GGCTTTGTGCCACTACTGAT
1 GGCTTTGTGCCACTATTGAT
* *
28608737 GGCTTTGTGCCGCTATTTAT
1 GGCTTTGTGCCACTATTGAT
*
28608757 GGCTTTGTGTCACTATTGAT
1 GGCTTTGTGCCACTATTGAT
*
28608777 GGCTTTGTACCACTATTGAT
1 GGCTTTGTGCCACTATTGAT
* * *
28608797 GGCTTCGTGCCACTACTCAT
1 GGCTTTGTGCCACTATTGAT
28608817 GGCTTTGTGCCA
1 GGCTTTGTGCCA
28608829 TATACTGATA
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 98 1.00
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.39
Consensus pattern (20 bp):
GGCTTTGTGCCACTATTGAT
Found at i:28612889 original size:43 final size:43
Alignment explanation
Indices: 28612734--28612890 Score: 149
Period size: 43 Copynumber: 3.7 Consensus size: 43
28612724 TGTGTTTTTG
* * * *
28612734 TGTAAGACCACATCTGGAACGTTGGCATCGACTA-ATGATTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGA-TTACA
* * * *** *
28612778 TGTAAGACCATGTTTGGGACATCAACATCG-TATTTGATTTCA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTACA
* *
28612820 TGTAAGACCCCGTCTGGGATAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCACGTCTGGGA-CGTTGGCATCGATATTTGATTACA
28612863 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
28612891 TGTACGTGCT
Statistics
Matches: 87, Mismatches: 22, Indels: 9
0.74 0.19 0.08
Matches are distributed among these distances:
42 27 0.31
43 38 0.44
44 22 0.25
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTACA
Done.